The fallout over the resignation of Michael T. Flynn, President Trump's national security adviser, is still settling over Washington. Reporting by my colleagues on Monday night seemed to make Flynn's position in the White House untenable. They revealed that officials from the Justice Department had warned the Trump administration that Flynn had likely misled the White House regarding his conversations with the Russian ambassador — and that he was potentially vulnerable to Kremlin blackmail. After a steady drumbeat of speculation, Flynn tendered his resignation just before midnight.

Democratic politicians — and even some Republicans in Congress — are urging an investigation into the Flynn affair and the Trump camp's wider connections to Russia. After all, two other top Trump aides left their posts ahead of last year's election likely because of ties to Moscow.

Michael Flynn leaving the administration isn't enough to clear up questions that many of us have about the Trump team’s ties with Russia.

It's likely that Trump's fire-and-brimstone rhetoric about the war against "radical Islam," and his seeming declaration of a clash of civilizations, is in part informed by the views of Flynn and other zealots in the administration.

Flynn, Bannon and others have all, at various points, warned about a phantom Islamic takeover of the United States. In their zeal to crush jihadism, they train their attacks on Islam — a religion of more than a billion adherents — as a whole.

"Islam is not a real religion, but a political ideology masked behind a religion," Flynn claimed. He has repeatedly raged against the supposed "political correctness" of those who fear his rhetoric may alienate millions of Muslims, including American citizens.

The key distinction between the outlook of the Flynns and Bannons of the world and their predecessors in earlier administrations is that the former genuinely believe radical groups like the Islamic State represent the real face of Islam. The latter generally treated jihadists as aberrations who gained power amid the dysfunction of failing states.

Syrian opposition fighters say these unidentified men pictured north of Raqqa in early 2016 were members of US special operations. (Delil Souleiman/AFP)

What's different is the all-out embrace of a culture war, which seems at this point to be the signature political tactic of the Trump administration. You can draw a straight line from the extreme views of Flynn and others in the White House to Trump's travel ban on refugees and immigrants from seven Muslim-majority countries — a move stymied in the courts in part because it reflected thinly-veiled bigotry.

That Flynn's views didn't automatically disqualify him from such a vital and strategic post in the world's most powerful government speaks volumes about the deep Islamophobia within the Trump administration. Not surprisingly, Muslim rights groups cheered Flynn's departure on Tuesday.

"We welcome Michael Flynn's resignation and hope it is followed by that of all the other anti-Muslim bigots currently formulating domestic and international policies in the White House, including Steve Bannon, Stephen Miller and Sebastian and Katharine Gorka," said Nihad Awad of the Council on American-Islamic Relations, in a statement."Our nation is best served by those who base their policy recommendations on facts, not fear."